The genome sequence of the London Dowd, Blastobasis lacticolella (Rebel, 1939) [version 1; peer review: awaiting peer review]

We present a genome assembly from an individual male Blastobasis lacticolella (the London Dowd; Arthropoda; Insecta; Lepidoptera; Blastobasidae). The genome sequence is 577.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,302 protein coding genes.


Background
Thirty-three species of the genus Blastobasis are known in Europe, and most of which are endemic to Madeira (De Prins et al., 2009). Five species of Blastobasis Zeller, 1855 have been recorded in Britain and Ireland, all of which have been introduced here. All species in the genus rest with their wings held overlapping and wrapped around the abdomen, giving them a distinctive resting posture (Sterling et al., 2012). Blastobasis lacticolella was introduced to the west of mainland Europe accidentally, and there are now records from the Netherlands, Britain and Ireland. Since its introduction to the UK, it has spread rapidly and it is now found across most of Britain, but there are few records from much of Ireland, where it occurs mainly in coastal areas (GBIF Secretariat, 2022).
Blastobasis lacticolella is the largest of the Blastobasis species recorded in the UK, reaching 11 mm. The species is straw coloured, with varying degrees of brownish shading; lighter individuals should be instantly recognisable, while at the darker end of the spectrum they could be confused with light examples of B. vittata Wollaston, 1858, although the larger size and broader wings of lacticolella should help to distinguish it. B. lacticolella is further characterised by a dark streak or spot on the dorsum at 1/3, and two more dark spots alongside each other at around 2/3 (Sterling et al., 2012).
Like its relative B. adustella Walsingham, 1894, B. lacticolella larvae are highly polyphagous, feeding in silk tubes or spinnings on a variety of seeds and fruits as well as moss, dried leaves, oak galls and dead insects (Smart, 2021). They can be distinguished from the former species by their prothoracic plate, which is orange or brown as opposed to black. Larvae are active from June to August and again from September to May, with pupation occurring in June and August and the adults flying from mid-May through to December (Dickson, 2018).
We present a chromosomally complete genome sequence for Blastobasis lacticolella, based on one male specimen from Wytham Woods, Oxfordshire, as part of the Darwin Tree of Life Project. This project is a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland.

Genome sequence report
The genome was sequenced from one male Blastobasis lacticolella ( Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77, -1.33). A total of 32-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 63-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 87 missing joins or mis-joins and removed 32 haplotypic duplications, reducing the assembly length by 3.72% and the scaffold number by 50.56%, and increasing the scaffold N50 by 10.59%.
The final assembly has a total length of 577.1 Mb in 44 sequence scaffolds with a scaffold N50 of 20.5 Mb (Table 1). Most (99.91%) of the assembly sequence was assigned to 30 chromosomal-level scaffolds, representing 29 autosomes and the Z sex chromosome. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2- Figure 5; Table 2). While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited. The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/2561016.

Sample acquisition and nucleic acid extraction
A male Blastobasis lacticolella (specimen ID Ox000033, individual ilBlaLact1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.33) on 2019-06-29 using a light trap. The specimen was collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI). The ilBlaLact1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Tissue from the whole organism was disrupted using a Nippi Powermasher fitted with a BioMasher pestle. High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit. Low molecular weight DNA was removed from a 20 ng aliquot of extracted DNA using the 0.8X AMpure XP purification kit prior to 10X Chromium sequencing; a minimum of 50 ng DNA was submitted for 10X sequencing. HMW DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 30. Sheared DNA was purified by solid-phase reversible immobilisation using AMPure PB beads with a 1.8X ratio of beads to sample to remove the shorter fragments and concentrate the DNA sample. The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system.

Sequencing
Pacific Biosciences HiFi circular consensus and 10X Genomics read cloud DNA sequencing libraries were constructed according to the manufacturers' instructions. DNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II (HiFi) and HiSeq X Ten (10X) instruments. Hi-C data were also generated from remaining tissue of ilBlaLact1 using the Arima2 kit and sequenced on the HiSeq X Ten instrument.

Genome assembly, curation and evaluation
Assembly was carried out with HiCanu (Nurk et al., 2020) and haplotypic duplication was identified and removed with purge_dups (Guan et al., 2020). One round of polishing was performed by aligning 10X Genomics read data to the assembly with Long Ranger ALIGN, calling variants with FreeBayes (Garrison & Marth, 2012). The assembly was then scaffolded with Hi-C data (Rao et al., 2014) using SALSA2 (Ghurye et al., 2019. The assembly was checked for contamination and corrected using the gEVAL system (Chow et al., 2016) as described previously (Howe et al., 2021). Manual curation was performed using gEVAL, HiGlass (Kerpedjiev et al., 2018) and Pretext (Harry, 2022). The mitochondrial genome was assembled using MitoHiFi (Uliano-Silva et al., 2023), which runs MitoFinder (Allio et al., 2020) or MITOS (Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.   A Hi-C map for the final assembly was produced using bwa-mem2 (Vasimuddin et al., 2019) in the Cooler file format (Abdennur & Mirny, 2020). To assess the assembly metrics, the k-mer completeness and QV consensus quality values were calculated in Merqury . This work was done using Nextflow (Di Tommaso et al., 2017) DSL2 pipelines "sanger-tol/readmapping" (Surana et al., 2023a) and "sanger-tol/genomenote" (Surana et al., 2023b). The genome was analysed within the BlobToolKit environment (Challis et al., 2020) and BUSCO scores (Manni et al., 2021;Simão et al., 2015) were calculated. Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use. The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible. The overarching areas of consideration are: • Ethical review of provenance and sourcing of the material